From 88c421e8de791760e0267500be0790c706af63d0 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 5 Nov 2018 22:03:59 -0500
Subject: [PATCH] r881: a recent change reduces sr accuracy

---
 align.c | 2 --
 main.c  | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/align.c b/align.c
index 25b19d0..724debe 100644
--- a/align.c
+++ b/align.c
@@ -594,11 +594,9 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 		qs0 = 0, qe0 = qlen;
 		l = qs;
 		l += l * opt->a + opt->end_bonus > opt->q? (l * opt->a + opt->end_bonus - opt->q) / opt->e : 0;
-		l = l < opt->bw? l : opt->bw;
 		rs0 = rs - l > 0? rs - l : 0;
 		l = qlen - qe;
 		l += l * opt->a + opt->end_bonus > opt->q? (l * opt->a + opt->end_bonus - opt->q) / opt->e : 0;
-		l = l < opt->bw? l : opt->bw;
 		re0 = re + l < (int32_t)mi->seq[rid].len? re + l : mi->seq[rid].len;
 	} else {
 		// compute rs0 and qs0
diff --git a/main.c b/main.c
index 4845a87..eee5415 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.13-r880-dirty"
+#define MM_VERSION "2.13-r881-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>